Exporting 3D models for dynamic texture changes on web
The most popular format for web atm is GLTF, there is a Blender Addon for that.
Ofc. you cannot unwrap some vertices and ignore the rest, if you want separate UV Maps, you need separate objects (not files). Having an atlassed texture is always more perfomant than using multiple ones, not sure if that's an option in this case though. 
It's probably easiest to separate the parts into different objects, use different materials on each part and set their textures individually.  if your UV Layout alone is 5MB, consider decimating your objects either manually or by using the decimate modifier.